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idem-lab / conmat

Create Contact Matrices from Population Data
https://idem-lab.github.io/conmat/dev/
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Fitted rates numerically 0 occurred when fitting model in symmetric model #95

Closed njtierney closed 1 year ago

njtierney commented 1 year ago

In the symmetrical features PR, we get an error/warning about the model fit.

Note that this doesn’t happen on the previous master that doesn’t implement the symmetrical features

library(conmat)

polymod_population <- get_polymod_population()

synthetic_settings_5y_polymod <- extrapolate_polymod(
  population = polymod_population
)
#> Warning in bgam.fit(G, mf, chunk.size, gp, scale, gamma, method = method, :
#> fitted rates numerically 0 occurred

#> Warning in bgam.fit(G, mf, chunk.size, gp, scale, gamma, method = method, :
#> fitted rates numerically 0 occurred

Created on 2022-09-19 by the reprex package (v2.0.1)

Session Info ``` r sessioninfo::session_info() ``` ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.2.0 (2022-04-22) ## os macOS Monterey 12.3.1 ## system aarch64, darwin20 ## ui X11 ## language (EN) ## collate en_AU.UTF-8 ## ctype en_AU.UTF-8 ## tz Pacific/Auckland ## date 2022-09-19 ## pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## askpass 1.1 2019-01-13 [1] CRAN (R 4.2.0) ## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0) ## callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.0) ## cli 3.3.0.9000 2022-06-15 [1] Github (r-lib/cli@31a5db5) ## clipr 0.8.0 2022-02-22 [1] CRAN (R 4.2.0) ## credentials 1.3.2 2021-11-29 [1] CRAN (R 4.2.0) ## curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0) ## digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) ## evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.0) ## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) ## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) ## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) ## gert 1.7.0 2022-08-07 [1] CRAN (R 4.2.0) ## gh 1.3.0 2021-04-30 [1] CRAN (R 4.2.0) ## gitcreds 0.1.1 2020-12-04 [1] CRAN (R 4.2.0) ## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) ## highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) ## htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) ## httr 1.4.3 2022-05-04 [1] CRAN (R 4.2.0) ## jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0) ## knitr 1.40 2022-08-24 [1] CRAN (R 4.2.0) ## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) ## openssl 2.0.2 2022-05-24 [1] CRAN (R 4.2.0) ## pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0) ## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) ## processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.0) ## ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) ## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) ## R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) ## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) ## R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) ## R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0) ## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) ## reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) ## rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0) ## rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.0) ## rmdgh 0.3.0 2022-09-10 [1] https://milesmcbain.r-universe.dev (R 4.2.1) ## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) ## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) ## stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) ## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) ## styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) ## sys 3.4 2020-07-23 [1] CRAN (R 4.2.0) ## tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) ## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) ## vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) ## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) ## xfun 0.32.1 2022-08-11 [1] https://yihui.r-universe.dev (R 4.2.0) ## yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) ## ## [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library ## ## ──────────────────────────────────────────────────────────────────────────────
njtierney commented 1 year ago

This no longer occurs in #105 

library(conmat)

polymod_population <- get_polymod_population()

synthetic_settings_5y_polymod <- extrapolate_polymod(
  population = polymod_population
)

Created on 2022-12-12 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.1 (2022-06-23) #> os macOS Monterey 12.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Brisbane #> date 2022-12-12 #> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) #> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1) #> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0) #> conmat * 0.0.0.9004 2022-12-12 [1] local #> countrycode 1.4.0 2022-05-04 [1] CRAN (R 4.2.0) #> curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.0) #> data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0) #> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0) #> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.0) #> dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.2.0) #> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fields 14.1 2022-08-12 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> furrr 0.3.1 2022-08-15 [1] CRAN (R 4.2.0) #> future 1.29.0 2022-11-06 [1] CRAN (R 4.2.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) #> ggplot2 3.4.0 2022-11-04 [1] CRAN (R 4.2.0) #> globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.1) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0) #> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) #> httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0) #> jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.2.0) #> knitr 1.41 2022-11-18 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> maps 3.4.1 2022-10-30 [1] CRAN (R 4.2.0) #> Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0) #> mgcv 1.8-41 2022-10-21 [1] CRAN (R 4.2.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) #> nlme 3.1-160 2022-10-10 [1] CRAN (R 4.2.0) #> oai 0.4.0 2022-11-10 [1] CRAN (R 4.2.0) #> parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.0) #> purrr * 0.3.5 2022-10-06 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0) #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0) #> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0) #> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> socialmixr 0.2.0 2022-10-27 [1] CRAN (R 4.2.0) #> spam 2.9-1 2022-08-07 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) #> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0) #> styler 1.8.1 2022-11-07 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> tidyr 1.2.1 2022-09-08 [1] CRAN (R 4.2.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) #> timechange 0.1.1 2022-11-04 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.0) #> viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.0) #> viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> wpp2017 1.2-3 2020-02-10 [1] CRAN (R 4.2.0) #> xfun 0.35 2022-11-16 [1] CRAN (R 4.2.0) #> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0) #> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

Closing this issue